Are both babies rear-facing? If yes, you might not have much choice but to get the 7-seater and put the babies in the 2nd row middle and outboard positions. That allows one remaining 2nd row seat to slide forward and give access to the 3rd row but it'll be cramped for anyone sitting in the 3rd row. Rear-facing seats will not fit in the 3rd row.
However... if at least one of the children is front-facing, then go with the 6-seater. With 6-seater, the front-facing child can sit in the 3rd row (allowing one 2nd row outboard seat to serve as entry/exit point) or the front-facing child can sit in the 2nd row (when unoccupied the child seat can still slide forward to provide access to the 3rd row). More importantly, a parent sitting in any position in the 2nd or 3rd row has relatively easy access to both children in case they need to be attended to during a long drive. And 3rd row adults have much more leg room and more options for entering and exiting the 3rd row.